| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2022-08-10 | pylint fixes | Alexander_Kabui | |
| 2022-08-10 | code refactoring | Alexander_Kabui | |
| 2022-08-10 | remove unnessary code | Alexander_Kabui | |
| 2022-08-10 | remove unnecessary parsing of floats | Alexander_Kabui | |
| 2022-08-10 | merge for results | Alexander_Kabui | |
| 2022-08-10 | enhancements for rust tissue | Alexander_Kabui | |
| 2022-08-03 | Refactor: Remove unnecessary whitespace and name | Frederick Muriuki Muriithi | |
| 2022-08-03 | Refactor: Remove unnecessary iterations and name | Frederick Muriuki Muriithi | |
| * remove extra iteration that is unnecessary * remove unnecessary variables | |||
| 2022-07-29 | Fix failing tests | Frederick Muriuki Muriithi | |
| * gn3/computations/correlations.py: rename function * mypy.ini: deactivate mypy error about missing imports * tests/integration/test_correlation.py: mock correct function * tests/unit/computations/test_correlation.py: test correct function | |||
| 2022-07-28 | Update sample correlations code to use multiprocessing | Frederick Muriuki Muriithi | |
| * To help speed up the processing of the correlations, convert the `compute_all_sample_correlation` function to use the multiprocessing module. | |||
| 2022-07-22 | mypy fixes | Alexander_Kabui | |
| 2022-07-22 | pep8 fixes | Alexander_Kabui | |
| 2022-07-22 | linting and tests fixes | Alexander_Kabui | |
| 2022-07-22 | compute num overlap | Alexander_Kabui | |
| 2022-07-22 | fix for bug splitting list data | Alexander_Kabui | |
| 2022-07-22 | minor fixes for parsing data | Alexander_Kabui | |
| 2022-07-22 | code to parse tissue correlation input | Alexander_Kabui | |
| 2022-07-22 | mypy pylint fixes | Alexander_Kabui | |
| 2022-07-22 | code to fetch correct sample corr data | Alexander_Kabui | |
| 2022-07-22 | delete dead_code;rename variables | Alexander_Kabui | |
| 2022-07-22 | minor fixes | Alexander_Kabui | |
| 2022-06-29 | use explicit parameters | Alexander_Kabui | |
| 2022-06-29 | fix issues | Alexander_Kabui | |
| 2022-06-29 | pylint fixes | Alexander | |
| 2022-06-29 | minor fixes | Alexander | |
| 2022-06-29 | handle tmp files generation | Alexander | |
| 2022-06-29 | parse output data | Alexander | |
| 2022-06-29 | pep8 formatting | Alexander | |
| 2022-06-29 | init rust correlation module | Alexander | |
| 2022-05-30 | Pass trait data as args to `fix_strains` and fix some bugs | Frederick Muriuki Muriithi | |
| The `fix_strains` function works on the trait data, not the basic trait info. This commit fixes the arguments passed to the function, and also some bugs in the function. | |||
| 2022-05-24 | New script to compute partial correlations | Frederick Muriuki Muriithi | |
| * Add a new script to compute the partial correlations against: - a select list of traits, or - an entire dataset depending on the specified subcommand. This new script is meant to supercede the `scripts/partial_correlations.py` script. * Fix the check for errors * Reorganise the order of arguments for the `partial_correlations_with_target_traits` function: move the `method` argument before the `target_trait_names` argument so that the common arguments in the partial correlation computation functions share the same order. | |||
| 2022-05-21 | Use multiprocessing to improve performance | Frederick Muriuki Muriithi | |
| 2022-05-21 | Process primary, target and control traits in a single iteration | Frederick Muriuki Muriithi | |
| Rework the code to process the traits in a single iteration to improve performance. | |||
| 2022-05-21 | Return generator object rather than tuples | Frederick Muriuki Muriithi | |
| Return generator objects rather than pre-computed tuples to reduce the number of iterations needed to process the data, and thus improve the performance of the system somewhat. | |||
| 2022-05-06 | Fix linting and typing errors | Frederick Muriuki Muriithi | |
| 2022-05-06 | Hook up pcorrs with target traits computations | Frederick Muriuki Muriithi | |
| Enable the endpoint to actually compute partial correlations with selected target traits rather than against an entire dataset. Fix some issues caused by recent refactor that broke pcorrs against a dataset | |||
| 2022-05-05 | Compute partial correlation with selected traits | Frederick Muriuki Muriithi | |
| Compute partial correlations against a selection of traits rather than against an entire dataset. | |||
| 2022-05-05 | Extract common error checking. Rename function. | Frederick Muriuki Muriithi | |
| * Extract the common error checking code into a separate function * Rename the function to make its use clearer | |||
| 2022-05-03 | Refactor: Remove unnecessary loop | Frederick Muriuki Muriithi | |
| Remove an unnecessary looping construct to help with speeding up the partial correlations somewhat. | |||
| 2022-03-29 | Remove unused module | Frederick Muriuki Muriithi | |
| * Remove a module that is no longer in use | |||
| 2022-03-23 | Run python-black on file and fix other pylint issues. | BonfaceKilz | |
| See: <https://ci.genenetwork.org/jobs/genenetwork3-pylint/126> * gn3/computations/rqtl.py: Run `black gn3/computations/rqtl.py`. Also, manually fix other pylint issues. | |||
| 2022-03-22 | Fixes pylint errors | zsloan | |
| 2022-03-22 | Fixed mypy typing errors | zsloan | |
| 2022-03-22 | Tried to make the docstrings more consistent | zsloan | |
| 2022-03-22 | Add typing to some functions | zsloan | |
| 2022-03-22 | Add functions for getting proximal/distal markers for each pseudomarker ↵ | zsloan | |
| position in pair-scan results + return only the sorted top 500 results | |||
| 2022-03-22 | Added genofile name to inputs for processing R/qtl pair-scan results, since ↵ | zsloan | |
| it's needed to store the proximal/distal markers for each position | |||
| 2022-03-22 | Removed quotes from beginning and end of chromosome string | zsloan | |
| 2022-03-22 | Fixed a cople function calls to use the updated function names | zsloan | |
| 2022-03-22 | Create pairscan_for_figure and pairscan_for_table functions that return the ↵ | zsloan | |
| Dict and List respectively used for the pair scan figure and the table showing the results | |||
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